Genome analysis of cellulose and hemicellulose degrading Micromonospora sp. CP22

Chen, Sye Jinn; Lam, Ming Quan; Thevarajoo, Suganthi; Manan, Fazilah Abd; Yahya, Adibah; Chong, Chun Shiong

doi:10.1007/s13205-020-2148-z

Cited by 13 publications

(8 citation statements)

References 40 publications

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“…These three enzymes containing genes are identified by dbCAN2 meta server for the prediction of CAZyme such as GH5, GH6, GH9 and GH12 (endoglucanase), GH6, GH9 and GH48 (exoglucanase) and GH1 and GH3(β-glucosidase) which are found in Lentzea sp. and are similar with other genera 48,49 48 . All of these GH families are found in Lentzea such asendo-1,4-β-xylanase (GH5, GH8, GH10, GH11, GH30, GH43, GH48), β-xylosidase (GH39, and GH43), α-arabinofuranosidase (GH12, GH43, GH51, and GH62) and other xylanase is acetyl xylan esterase (CE1, CE3 and CE7) and polysaccharide deacetylase (CE4), respectively.…”

Section: Discussionsupporting

confidence: 84%

“…The modAA domain is engaged for modification of the incorporated amino acid 37 . These six classes were matched with pathways associated with the biosynthesis of microcystin (164), syringomycin (99), actinomycin (51), calcium-dependent antibiotic (49), bleomycin (32), cyclomarin (27), bacillibactin (21), bacitracin (19), complestatin (7), cyclosporin (7), fengycin (4), gramicidin (1), iturin (7), lychenicin (8), mycosubtilin (8), pksnrps2 (3), pristinamycin (12), pyochelin (8), thiocoraline (6), tyrocidine (17), yersiniabactin ( 11) sporolide (1), and surfactin ( 6) but with very low sequence similarity (average of 41%) indicating their association with different compounds. Functional classification depicted that total 524 KS domains present in each of the Lentzea genomes which are distributed in nine classes, among them most are from modular class and the rest of them are trans, PUFA, KS1, hybrid KS, iterative, FAS, and enediyne.…”

Section: Ribosomally Synthesized and Post-translationally Modified Pe...mentioning

confidence: 99%

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Comprehensive genome analysis of Lentzea reveals repertoire of polymer-degrading enzymes and bioactive compounds with clinical relevance

Maiti

Mandal

2022

Sci Rep

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The genus Lentzea is a rare group of actinobacteria having potential for the exploration of bioactive compounds. Despite its proven ability to produce compounds with medical relevance, Lentzea genome analysis remains unexplored. Here we show a detailed understanding of the genetic features, biosynthetic gene clusters (BGCs), and genetic clusters for carbohydrate-active enzymes present in the Lentzea genome. Our analysis determines the genes for core proteins, non-ribosomal peptide synthetase condensation domain, and polyketide synthases-ketide synthase domain. The antiSMASH-based sequence analysis identifies 692 BGCs among which 8% are identical to the BGCs that produce geosmin, citrulassin, achromosin (lassopeptide), vancosamine, anabaenopeptin NZ857/nostamide A, alkylresorcinol, BE-54017, and bezastatin. The remaining BGCs code for advanced category antimicrobials like calcium-dependent, glycosylated, terpenoids, lipopeptides, thiopeptide, lanthipeptide, lassopeptide, lingual antimicrobial peptide and lantibiotics together with antiviral, antibacterial, antifungal, antiparasitic, anticancer agents. About 28% of the BGCs, that codes for bioactive secondary metabolites, are exclusive in Lentzea and could lead to new compound discoveries. We also find 7121 genes that code for carbohydrate-degrading enzymes which could essentially convert a wide range of polymeric carbohydrates. Genome mining of such genus is very much useful to give scientific leads for experimental validation in the discovery of new-generation bioactive molecules of biotechnological importance.

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Section: Discussionsupporting

confidence: 84%

Section: Ribosomally Synthesized and Post-translationally Modified Pe...mentioning

confidence: 99%

Comprehensive genome analysis of Lentzea reveals repertoire of polymer-degrading enzymes and bioactive compounds with clinical relevance

Maiti

Mandal

2022

Sci Rep

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“…The identification and annotation of strain M1816 CAZymes were based on the Carbohydrate-active enzymes database (CAZy, http://www.cazy.org/, 2 July 2021) and performed on the automated Carbohydrate-active enzyme ANnotation (dbCAN2, http: //cys.bios.niu.edu/dbCAN2, 21 July 2021) meta server [43], which integrates three stateof-the-art tools for CAZome (i.e., all CAZymes of a genome) annotation: (i) HMMER (biosequence analysis using profile hidden Markov models, http://www.hmmer.org/, 21 July 2021) search against the dbCAN HMM (hidden Markov model) database; (ii) DI-AMOND search against the CAZy pre-annotated CAZyme sequence database; and (iii) Hotpep search against the conserved CAZyme short peptide database. This was followed by a further screening on the identified CAZyme based on the principle that the CAZy domains were recognized by at least two of the three tools (DIAMONDS, HMMER, and Hotpep) [44]. The genes predicted by dbCAN2 were manually verified by means of BLAST against the NR (non-redundant protein sequences) database.…”

Section: Cazymes Identificationmentioning

confidence: 99%

Enzyme Production Potential of Penicillium oxalicum M1816 and Its Application in Ferulic Acid Production

Zhang

Liu

Hai-long

et al. 2021

Foods

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The present study focused on isolating an efficient enzyme production microorganism for ferulic acid (FA) production from wheat bran. A wild-type cellulase-, xylanase-, and feruloyl esterase-producing strain was isolated and identified as Penicillium oxalicum M1816. The genome was sequenced and assembled into 30.5 Mb containing 8301 predicted protein-coding genes. In total, 553 genes were associated with carbohydrate metabolism. Genomic CAZymes analysis indicated that P. oxalicum M1816, comprising 39 cellulolytic enzymes and 111 hemicellulases (including 5 feruloyl esterase genes), may play a vital role in wheat bran degradation and FA production. The crude enzyme of strain M1816 could release 1.85 ± 0.08 mg·g−1 FA from de-starched wheat bran (DSWB) at 12 h, which was significantly higher than other commercial enzymes. Meanwhile, when the strain M1816 was cultured in medium supplemented with DSWB, up to 92.89% of the total alkali-extractable FA was released. The process parameters of solid-state fermentation were optimized to enhance enzyme production. The optimized wheat bran Qu of P. oxalicum M1816 was applied to huangjiu fermentation, and the FA content was increased 12.4-fold compared to the control group. These results suggest that P. oxalicum M1816 is a good candidate for the development of fermented foods bio-fortified with FA.

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“…The ability of Micromonospora spp. to depolymerize the lignocellulosic biomass is relatively less studied compared to other genera from actinobacteria (Chen et al 2020). The ability of Micromonospora spp.…”

Section: Discussionmentioning

confidence: 99%

Increase in Polyphenolic Substances from Fermented Robusta Coffee Pulp (Coffea canephora L.) by Using Indigenous Actinomycetes

et al. 2023

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The fermentation of the coffee fruit processing into coffee beans leaves the fermented coffee pulp which still contains polyphenol secondary metabolites. This study aimed to analyze the total flavonoid content (TFC) and total phenolic content (TPC) of fermented robusta coffee pulp (Coffea canephora L.) by using indigenous Actinomycetes. The ability of fermented extracts to inhibit free radical DPPH (2,2-diphenyl-1-picrylhydrazyl) also were done. In this study, coffee cherries were fermented in the solid-state fermentation cultivation (SSF) using isolates HJ4.5b, P2b(b).3 and P2b(b).18 which in previous studies were reported to have cellulolytic and xylanolytic activities. Determination of molecular identification base on 16S rRNA gen showed the isolates HJ4.5b and P2b(b).3 have similarities to the genus Streptomycetes, while P2b(b).18 has a homologous base arrangement with a rare actinomycetes genus Micromonospora. Fermentation using P2b(b).3 on the 9th day of fermentation indicated the highest percentage increase in TFC (295.54%) with IC50 18.41 µl/ml and having an antioxidant activity index (AAI) value of 2.14 which was included in the very strong antioxidant activity category.

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Genome analysis of cellulose and hemicellulose degrading Micromonospora sp. CP22

Cited by 13 publications

References 40 publications

Comprehensive genome analysis of Lentzea reveals repertoire of polymer-degrading enzymes and bioactive compounds with clinical relevance

Comprehensive genome analysis of Lentzea reveals repertoire of polymer-degrading enzymes and bioactive compounds with clinical relevance

Enzyme Production Potential of Penicillium oxalicum M1816 and Its Application in Ferulic Acid Production

Increase in Polyphenolic Substances from Fermented Robusta Coffee Pulp (Coffea canephora L.) by Using Indigenous Actinomycetes

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